Thats why ZC and imps have units to negate projectiles, its to counter rebels. If this is true we must look at how and why projectiles affect each faction.
Lets first look at Rebels vs ZC. The reason Gunboats are so effective is because their ships cannot counter the gunboats as well as the sheer laser power of the imps. The ZC uses mass drivers and special weapons. These are effective against bombers (mass drivers own B-Wings and other fighters) and Aggressor cannons are slow, even without boosted engines, one can avoid the blasts with a little micro. The ZC has very few ships emphasizing on ion cannons and lasers.(which the gunboats are weak against) Gunboats are also somewhat immune to self destructs. Gunboats can easily run from a dying aggressor or vengeance. Even if you dont run, if you space them out, the blast might only kill 1-2. Against Kedalbes gunboats are somewhat immune to its special ability. Draining the weak shield on a gunboat wont help it much. By staying on one side of the Kedalbe a couple gunships can rip apart the turbo lasers making the kedalbe very weak. As I said before, Gunboats are fast naturally. Keeping to one side and flanking the capital is easy. Hard point destruction should be Turbo laser->Mass Driver->Ion Cannon->Special Weapon->change sides. Leave the shield generator (the husk of a ship is now wasting 4 unit slots) Because of these weaknesses, the ZC has come up with the Crusader's point defense laser system. So in order to have an effective gunboat fleet, one must bring something the size of a Neb-B or bigger to take care of crusaders. Mon cals are expensive and slow Speed is key for this tactic.

Summing up:
Why are ZC weak against Gunboats?
-Hard to destroy them
-Few counters
-Easy to control mines
-ZC ships excel at eliminating Small fighters and Large capitals, but not intermediate ships.

Now, let us examine the Imperial fleet.
What do I see on the Acclamator? Turbo Lasers, concussion missiles, proton torpedoes and the standar hanger, shields and engines. Their progectile weapons wont last long because these ships are relatively weak. now what about the Victory? Same thing, tough ship....but an added ion cannon. And Thrawn, Piet and the ISD? One more ion cannon and a tractor beam. Now....what do you think the Imperial Tactic will be?

Overwhelm with raw Laser power....

This is extremly powerful against Medium ships hence why Gunboats and imperials do not mix. Imperials can simply over run any opponent with sheer numbers because their fighters are garrison. However they too have a weakness. Proton torpedoes. Concussion missiles only come from the gunboat and thats out of the question. So who ya gonna call?! Not the ghost busters...but the B-Wings! Now why B-Wings over MC30s? Lets look at what an MC30 is. Its bigger than a corvette and smaller than a Liberty....its a medium ship. I dont care what the game says its strength are, ISD WILL OWN THEM. ISD will kill the MC30 or just knock out the 2 torpedo launchers before it can inflict any real damage. Knock out those 2 hard points and you just sent the Rebels into a 4000 credit debt! B-Wings are fast, and very effective against Imperial Capitals. The turbo lasers cant target the small fighters and garisson fighters are relatively weak. What is the Imp counter to The Bladewing? The Broadside and the Interdictor. In my experience, interdictors are excelent, but too weak. A moncal with the other side turned and boosting its shields can easily eliminate them. Broadsides are your best bet. Again, if the B-wings are destroyed, they cant hurt you. Broadsides can take out multiple squads of B-Wings with one stream of Diamond Borron Missiles. Now how does a Rebel counter this if the broadside is waaaaayyyy at the back of the Imp fleet? Get Han to do it solo, thats how. Pop on invulnerability and fly into the belly of the beast. Make a gunship quick and hyper it in right behind the broadside/s. Han and the gunships should make quick work of them. If you want it done faster, make 2 gunships.

No Broadside=healthy B-wings=victory.
Oh and you will need marauders in your back line to take care of the swarms of fighters. Of course the Imps can just scout your back line and hyper in an acclamator to squash the marauders, but they probebly wont be thinking of that with B-Wings pounding on Piet.

Summing up:
Why are Imps weak against B-Wings?
-Hard to destroy them
-Few counters (I didnt mention Tartans....dont use them, they will get eaten by the Mon Cals)
-Deals massive damage against capitals.
-Imps are good at eliminating medium ships, but not large or small.

I wont state any build orders as each map is different and ill let you experirment for yourselves (if you like these tactics).
And remember, this is only explaining key units, Im not trying to say my fleets are made of 25 B-wings or 12 gunboats, more like,